## Error in library(future.apply) : 
##   there is no package called 'future.apply'

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

Canonic Transcript dynamics (TSS ~ TES)

Those reads were counted only, where both the 3-prime AND the 5-prime adapters were “correct” (according to LoRTIA)

When counting with either adapters, the clustering grouped ORF64 together with two late genes

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.2)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.48)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.67)... Done.
## Bootstrap (r = 0.78)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.07)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.37)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  2:       1    ORF2 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  3:       1    ORF3 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  4:       1    ORF4 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  5:       1    ORF8 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  6:       1    ORF9 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  7:       1   ORF11 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  8:       1   ORF14 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  9:       1   ORF18 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 10:       1   ORF19 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 11:       1   ORF20 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 12:       1   ORF21 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 13:       1   ORF22 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 14:       1   ORF23 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 15:       1   ORF24 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 16:       1   ORF25 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 17:       1   ORF26 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 18:       1   ORF28 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 19:       1   ORF29 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 20:       1   ORF31 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 21:       1   ORF33 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 22:       1   ORF34 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 23:       1 ORF35.5 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 24:       1   ORF36 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 25:       1   ORF37 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 26:       1   ORF38 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 27:       1   ORF39 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 28:       1     CTO 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 29:       1   ORF40 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 30:       1   ORF42 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 31:       1   ORF43 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 32:       1   ORF44 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 33:       1   ORF46 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 34:       1   ORF49 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 35:       1   ORF50 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 36:       1   ORF51 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 37:       1   ORF58 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 38:       1   ORF61 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 39:       1   ORF62 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 40:       1 ORF64_1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 41:       1 ORF66_1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 42:       1   ORF68 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 43:       1   ORF73 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 44:       1   ORF74 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 45:       1   ORF75 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 46:       1   ORF76 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 47:       2    ORF5 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 48:       2    ORF7 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 49:       2   ORF10 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 50:       2   ORF17 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 51:       2   ORF30 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 52:       2   ORF53 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 53:       2   ORF63 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 54:       2  NOIR_2 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 55:       3    ORF6 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 56:       3 ORF65_1 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 57:       3 ORF67_1 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 58:       4   ORF12 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 59:       4   ORF13 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 60:       4   ORF15 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 61:       4   ORF16 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 62:       4   ORF27 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 63:       4   ORF32 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 64:       4   ORF35 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 65:       4   ORF41 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 66:       4   ORF48 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 67:       4   ORF52 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 68:       4   ORF54 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 69:       4   ORF57 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 70:       4   ORF59 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 71:       4   ORF60 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 72:       4  NOIR_1 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 73:       4   ORF71 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 74:       4   ORF72 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 75:       5   ORF69 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 76:       5   ORF70 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c         pchi
##           <num>      <num>     <num>        <num>
##  1: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  2: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  3: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  4: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  5: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  6: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  7: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  8: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  9: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 10: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 11: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 12: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 13: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 14: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 15: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 16: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 17: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 18: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 19: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 20: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 21: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 22: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 23: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 24: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 25: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 26: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 27: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 28: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 29: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 30: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 31: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 32: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 33: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 34: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 35: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 36: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 37: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 38: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 39: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 40: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 41: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 42: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 43: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 44: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 45: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 46: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 47: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 48: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 49: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 50: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 51: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 52: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 53: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 54: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 55: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 56: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 57: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 58: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 59: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 60: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 61: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 62: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 63: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 64: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 65: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 66: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 67: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 68: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 69: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 70: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 71: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 72: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 73: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 74: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 75: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 76: 0.005276687 -0.4807824 0.5462305 0.0847886099
##           se.bp          v         c         pchi

##  [1] "ORF25"   "ORF35.5" "ORF58"   "ORF50"   "ORF64_1" "ORF42"   "ORF33"  
##  [8] "ORF34"   "ORF62"   "ORF4"    "ORF20"   "ORF21"   "ORF61"   "ORF31"  
## [15] "ORF1"    "NOIR_1"  "ORF32"   "ORF59"   "ORF69"
## [1] 19
##  [1] "ORF12"  "ORF13"  "ORF15"  "ORF16"  "ORF27"  "ORF32"  "ORF35"  "ORF41" 
##  [9] "ORF48"  "ORF52"  "ORF54"  "ORF57"  "ORF59"  "ORF60"  "NOIR_1" "ORF71" 
## [17] "ORF72"  "ORF69"  "ORF70"
## [1] 19

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  2:       1    ORF2 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  3:       1    ORF3 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  4:       1    ORF4 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  5:       1    ORF8 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  6:       1    ORF9 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  7:       1   ORF11 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  8:       1   ORF14 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  9:       1   ORF18 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 10:       1   ORF19 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 11:       1   ORF20 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 12:       1   ORF21 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 13:       1   ORF22 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 14:       1   ORF23 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 15:       1   ORF24 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 16:       1   ORF25 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 17:       1   ORF26 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 18:       1   ORF28 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 19:       1   ORF29 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 20:       1   ORF31 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 21:       1   ORF33 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 22:       1   ORF34 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 23:       1 ORF35.5 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 24:       1   ORF36 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 25:       1   ORF37 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 26:       1   ORF38 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 27:       1   ORF39 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 28:       1     CTO 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 29:       1   ORF40 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 30:       1   ORF42 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 31:       1   ORF43 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 32:       1   ORF44 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 33:       1   ORF46 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 34:       1   ORF49 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 35:       1   ORF50 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 36:       1   ORF51 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 37:       1   ORF58 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 38:       1   ORF61 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 39:       1   ORF62 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 40:       1 ORF64_1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 41:       1 ORF66_1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 42:       1   ORF68 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 43:       1   ORF73 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 44:       1   ORF74 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 45:       1   ORF75 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 46:       1   ORF76 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 47:       2    ORF5 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 48:       2    ORF7 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 49:       2   ORF10 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 50:       2   ORF17 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 51:       2   ORF30 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 52:       2   ORF53 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 53:       2   ORF63 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 54:       2  NOIR_2 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 55:       3    ORF6 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 56:       3 ORF65_1 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 57:       3 ORF67_1 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 58:       4   ORF12 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 59:       4   ORF13 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 60:       4   ORF15 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 61:       4   ORF16 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 62:       4   ORF35 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 63:       4   ORF41 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 64:       4   ORF48 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 65:       4   ORF52 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 66:       4   ORF54 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 67:       4   ORF57 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 68:       4   ORF60 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 69:       4   ORF71 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 70:       4   ORF72 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 71:       5   ORF27 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 72:       5   ORF32 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 73:       5   ORF59 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 74:       5  NOIR_1 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 75:       6   ORF69 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 76:       6   ORF70 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c         pchi
##           <num>      <num>     <num>        <num>
##  1: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  2: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  3: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  4: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  5: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  6: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  7: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  8: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  9: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 10: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 11: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 12: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 13: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 14: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 15: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 16: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 17: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 18: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 19: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 20: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 21: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 22: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 23: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 24: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 25: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 26: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 27: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 28: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 29: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 30: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 31: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 32: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 33: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 34: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 35: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 36: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 37: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 38: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 39: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 40: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 41: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 42: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 43: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 44: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 45: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 46: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 47: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 48: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 49: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 50: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 51: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 52: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 53: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 54: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 55: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 56: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 57: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 58: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 59: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 60: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 61: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 62: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 63: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 64: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 65: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 66: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 67: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 68: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 69: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 70: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 71: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 72: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 73: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 74: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 75: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 76: 0.005151284 -1.0361088 0.6760908 0.1863312328
##           se.bp          v         c         pchi

##  [1] "ORF43"   "ORF44"   "ORF25"   "ORF50"   "ORF64_1" "ORF35.5" "ORF58"  
##  [8] "ORF34"   "ORF4"    "ORF42"   "ORF33"   "ORF20"   "ORF21"   "ORF61"  
## [15] "ORF62"   "ORF31"   "ORF1"    "ORF69"
## [1] 18
##  [1] "ORF12"  "ORF13"  "ORF15"  "ORF16"  "ORF35"  "ORF41"  "ORF48"  "ORF52" 
##  [9] "ORF54"  "ORF57"  "ORF60"  "ORF71"  "ORF72"  "ORF27"  "ORF32"  "ORF59" 
## [17] "NOIR_1"
## [1] 17

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  2:       1    ORF4 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  3:       1    ORF9 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  4:       1   ORF19 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  5:       1   ORF20 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  6:       1   ORF21 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  7:       1   ORF31 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  8:       1   ORF34 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  9:       1   ORF37 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 10:       1   ORF38 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 11:       1   ORF49 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 12:       1   ORF50 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 13:       1   ORF51 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 14:       1   ORF61 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 15:       1 ORF64_1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 16:       2    ORF2 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 17:       2    ORF3 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 18:       2    ORF8 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 19:       2   ORF11 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 20:       2   ORF14 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 21:       2   ORF18 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 22:       2   ORF22 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 23:       2   ORF23 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 24:       2   ORF24 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 25:       2   ORF25 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 26:       2   ORF26 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 27:       2   ORF28 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 28:       2   ORF29 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 29:       2   ORF33 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 30:       2 ORF35.5 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 31:       2   ORF36 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 32:       2   ORF39 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 33:       2     CTO 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 34:       2   ORF40 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 35:       2   ORF42 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 36:       2   ORF43 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 37:       2   ORF44 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 38:       2   ORF46 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 39:       2   ORF58 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 40:       2   ORF62 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 41:       2 ORF66_1 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 42:       2   ORF68 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 43:       2   ORF73 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 44:       2   ORF74 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 45:       2   ORF75 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 46:       2   ORF76 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 47:       3    ORF5 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 48:       3    ORF7 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 49:       3   ORF10 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 50:       3   ORF17 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 51:       3   ORF30 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 52:       3   ORF53 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 53:       3   ORF63 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 54:       3  NOIR_2 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 55:       4    ORF6 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 56:       4 ORF65_1 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 57:       4 ORF67_1 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 58:       5   ORF12 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 59:       5   ORF13 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 60:       5   ORF15 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 61:       5   ORF16 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 62:       5   ORF35 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 63:       5   ORF41 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 64:       5   ORF48 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 65:       5   ORF52 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 66:       5   ORF54 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 67:       5   ORF57 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 68:       5   ORF60 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 69:       5   ORF71 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 70:       5   ORF72 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 71:       6   ORF27 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 72:       6   ORF32 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 73:       6   ORF59 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 74:       6  NOIR_1 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 75:       7   ORF69 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 76:       7   ORF70 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c         pchi
##           <num>      <num>     <num>        <num>
##  1: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  2: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  3: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  4: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  5: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  6: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  7: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  8: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  9: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 10: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 11: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 12: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 13: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 14: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 15: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 16: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 17: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 18: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 19: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 20: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 21: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 22: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 23: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 24: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 25: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 26: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 27: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 28: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 29: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 30: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 31: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 32: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 33: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 34: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 35: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 36: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 37: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 38: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 39: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 40: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 41: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 42: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 43: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 44: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 45: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 46: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 47: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 48: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 49: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 50: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 51: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 52: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 53: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 54: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 55: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 56: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 57: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 58: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 59: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 60: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 61: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 62: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 63: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 64: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 65: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 66: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 67: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 68: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 69: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 70: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 71: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 72: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 73: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 74: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 75: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 76: 0.005054755 -1.0403978 0.6004065 0.9714841967
##           se.bp          v         c         pchi

##  [1] "ORF61" "ORF21" "ORF19" "ORF49" "ORF31" "ORF1"  "ORF42" "ORF18" "ORF33"
## [10] "ORF62" "ORF69"
## [1] 11
##  [1] "ORF6"    "ORF65_1" "ORF67_1" "ORF12"   "ORF13"   "ORF15"   "ORF16"  
##  [8] "ORF35"   "ORF41"   "ORF48"   "ORF52"   "ORF54"   "ORF57"   "ORF60"  
## [15] "ORF71"   "ORF72"   "ORF69"   "ORF70"
## [1] 18

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  2:       1    ORF4 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  3:       1    ORF9 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  4:       1   ORF20 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  5:       1   ORF21 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  6:       1   ORF31 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  7:       1   ORF34 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  8:       1   ORF38 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  9:       1   ORF50 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 10:       1   ORF61 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 11:       1 ORF64_1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 12:       2    ORF2 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 13:       2    ORF3 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 14:       2   ORF11 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 15:       2   ORF14 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 16:       2   ORF18 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 17:       2   ORF26 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 18:       2   ORF28 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 19:       2   ORF29 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 20:       2   ORF39 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 21:       2   ORF40 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 22:       2 ORF66_1 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 23:       2   ORF73 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 24:       2   ORF75 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 25:       2   ORF76 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 26:       3    ORF5 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 27:       3    ORF7 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 28:       3   ORF10 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 29:       3   ORF17 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 30:       3   ORF30 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 31:       3   ORF53 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 32:       3   ORF63 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 33:       3  NOIR_2 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 34:       4    ORF6 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 35:       4 ORF65_1 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 36:       4 ORF67_1 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 37:       5    ORF8 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 38:       5   ORF22 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 39:       5   ORF23 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 40:       5   ORF25 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 41:       5   ORF33 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 42:       5 ORF35.5 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 43:       5   ORF36 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 44:       5     CTO 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 45:       5   ORF42 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 46:       5   ORF43 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 47:       5   ORF44 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 48:       5   ORF46 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 49:       5   ORF58 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 50:       5   ORF62 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 51:       6   ORF12 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 52:       6   ORF13 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 53:       6   ORF15 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 54:       6   ORF16 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 55:       6   ORF35 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 56:       6   ORF41 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 57:       6   ORF48 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 58:       6   ORF52 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 59:       6   ORF54 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 60:       6   ORF57 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 61:       6   ORF60 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 62:       6   ORF71 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 63:       6   ORF72 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 64:       7   ORF19 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 65:       7   ORF37 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 66:       7   ORF49 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 67:       7   ORF51 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 68:       8   ORF24 0.9958735 0.9993909 0.8730728 0.0010785300 0.0001980182
## 69:       8   ORF68 0.9958735 0.9993909 0.8730728 0.0010785300 0.0001980182
## 70:       8   ORF74 0.9958735 0.9993909 0.8730728 0.0010785300 0.0001980182
## 71:       9   ORF27 0.8123167 0.9712173 0.4422435 0.0233352327 0.0052517907
## 72:       9   ORF32 0.8123167 0.9712173 0.4422435 0.0233352327 0.0052517907
## 73:       9   ORF59 0.8123167 0.9712173 0.4422435 0.0233352327 0.0052517907
## 74:       9  NOIR_1 0.8123167 0.9712173 0.4422435 0.0233352327 0.0052517907
## 75:      10   ORF69 0.8623602 0.9872692 0.3384189 0.0203134193 0.0028130265
## 76:      10   ORF70 0.8623602 0.9872692 0.3384189 0.0203134193 0.0028130265
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c         pchi
##           <num>      <num>     <num>        <num>
##  1: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  2: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  3: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  4: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  5: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  6: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  7: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  8: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  9: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 10: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 11: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 12: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 13: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 14: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 15: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 16: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 17: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 18: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 19: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 20: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 21: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 22: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 23: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 24: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 25: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 26: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 27: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 28: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 29: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 30: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 31: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 32: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 33: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 34: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 35: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 36: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 37: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 38: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 39: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 40: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 41: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 42: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 43: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 44: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 45: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 46: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 47: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 48: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 49: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 50: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 51: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 52: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 53: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 54: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 55: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 56: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 57: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 58: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 59: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 60: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 61: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 62: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 63: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 64: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 65: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 66: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 67: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 68: 0.003852134 -2.1878185 1.0467811 0.0826112491
## 69: 0.003852134 -2.1878185 1.0467811 0.0826112491
## 70: 0.003852134 -2.1878185 1.0467811 0.0826112491
## 71: 0.005273787 -0.8768548 1.0221384 0.6101602138
## 72: 0.005273787 -0.8768548 1.0221384 0.6101602138
## 73: 0.005273787 -0.8768548 1.0221384 0.6101602138
## 74: 0.005273787 -0.8768548 1.0221384 0.6101602138
## 75: 0.005022019 -0.9087719 1.3255538 0.0684930061
## 76: 0.005022019 -0.9087719 1.3255538 0.0684930061
##           se.bp          v         c         pchi

## [1] "ORF1"  "ORF48" "ORF19" "ORF49" "ORF69"
## [1] 5
##  [1] "ORF6"    "ORF65_1" "ORF67_1" "ORF8"    "ORF22"   "ORF23"   "ORF25"  
##  [8] "ORF33"   "ORF35.5" "ORF36"   "CTO"     "ORF42"   "ORF43"   "ORF44"  
## [15] "ORF46"   "ORF58"   "ORF62"   "ORF19"   "ORF37"   "ORF49"   "ORF51"
## [1] 21

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  2:       1    ORF4 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  3:       1    ORF9 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  4:       1   ORF20 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  5:       1   ORF21 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  6:       1   ORF31 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  7:       1   ORF34 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  8:       1   ORF38 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  9:       1   ORF50 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 10:       1   ORF61 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 11:       2    ORF2 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 12:       2    ORF3 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 13:       2   ORF11 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 14:       2   ORF14 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 15:       2   ORF18 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 16:       2   ORF26 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 17:       2   ORF28 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 18:       2   ORF29 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 19:       2   ORF39 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 20:       2   ORF40 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 21:       2 ORF66_1 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 22:       2   ORF73 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 23:       2   ORF75 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 24:       2   ORF76 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 25:       3    ORF5 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 26:       3    ORF7 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 27:       3   ORF10 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 28:       3   ORF17 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 29:       3   ORF30 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 30:       3   ORF53 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 31:       3   ORF63 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 32:       3  NOIR_2 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 33:       4    ORF6 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 34:       4 ORF65_1 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 35:       4 ORF67_1 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 36:       5    ORF8 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 37:       5   ORF22 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 38:       5   ORF23 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 39:       5   ORF25 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 40:       5   ORF33 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 41:       5 ORF35.5 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 42:       5   ORF36 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 43:       5     CTO 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 44:       5   ORF42 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 45:       5   ORF43 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 46:       5   ORF44 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 47:       5   ORF46 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 48:       5   ORF58 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 49:       5   ORF62 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 50:       6   ORF12 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 51:       6   ORF13 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 52:       6   ORF15 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 53:       6   ORF16 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 54:       6   ORF35 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 55:       6   ORF41 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 56:       6   ORF48 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 57:       6   ORF52 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 58:       6   ORF54 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 59:       6   ORF57 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 60:       6   ORF60 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 61:       6   ORF71 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 62:       6   ORF72 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 63:       7   ORF19 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 64:       7   ORF37 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 65:       7   ORF49 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 66:       7   ORF51 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 67:       8   ORF24 0.9958735 0.9993909 0.8730728 0.0010785300 0.0001980182
## 68:       8   ORF68 0.9958735 0.9993909 0.8730728 0.0010785300 0.0001980182
## 69:       8   ORF74 0.9958735 0.9993909 0.8730728 0.0010785300 0.0001980182
## 70:       9   ORF27 0.8123167 0.9712173 0.4422435 0.0233352327 0.0052517907
## 71:       9   ORF32 0.8123167 0.9712173 0.4422435 0.0233352327 0.0052517907
## 72:       9   ORF59 0.8123167 0.9712173 0.4422435 0.0233352327 0.0052517907
## 73:      10 ORF64_1 0.8623602 0.9872692 0.3384189 0.0203134193 0.0028130265
## 74:      11  NOIR_1 0.7918505 0.9699239 0.4047690 0.0257680355 0.0055457572
## 75:      12   ORF69 0.7646666 0.9396246 0.5962335 0.0252573471 0.0091709615
## 76:      12   ORF70 0.7646666 0.9396246 0.5962335 0.0252573471 0.0091709615
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c         pchi
##           <num>      <num>     <num>        <num>
##  1: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  2: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  3: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  4: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  5: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  6: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  7: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  8: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  9: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 10: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 11: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 12: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 13: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 14: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 15: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 16: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 17: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 18: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 19: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 20: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 21: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 22: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 23: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 24: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 25: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 26: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 27: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 28: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 29: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 30: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 31: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 32: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 33: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 34: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 35: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 36: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 37: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 38: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 39: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 40: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 41: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 42: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 43: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 44: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 45: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 46: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 47: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 48: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 49: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 50: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 51: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 52: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 53: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 54: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 55: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 56: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 57: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 58: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 59: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 60: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 61: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 62: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 63: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 64: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 65: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 66: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 67: 0.003852134 -2.1878185 1.0467811 0.0826112491
## 68: 0.003852134 -2.1878185 1.0467811 0.0826112491
## 69: 0.003852134 -2.1878185 1.0467811 0.0826112491
## 70: 0.005273787 -0.8768548 1.0221384 0.6101602138
## 71: 0.005273787 -0.8768548 1.0221384 0.6101602138
## 72: 0.005273787 -0.8768548 1.0221384 0.6101602138
## 73: 0.005022019 -0.9087719 1.3255538 0.0684930061
## 74: 0.005200999 -0.8193269 1.0603490 0.2027475766
## 75: 0.005250522 -0.8976199 0.6540101 0.1100175114
## 76: 0.005250522 -0.8976199 0.6540101 0.1100175114
##           se.bp          v         c         pchi

## [1] "ORF48" "ORF19" "ORF49" "ORF69"
## [1] 4
##  [1] "ORF6"    "ORF65_1" "ORF67_1" "ORF8"    "ORF22"   "ORF23"   "ORF25"  
##  [8] "ORF33"   "ORF35.5" "ORF36"   "CTO"     "ORF42"   "ORF43"   "ORF44"  
## [15] "ORF46"   "ORF58"   "ORF62"   "ORF19"   "ORF37"   "ORF49"   "ORF51"  
## [22] "ORF69"   "ORF70"
## [1] 23

Selected number of clusters: 12

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  2:       1    ORF4 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  3:       1    ORF9 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  4:       1   ORF20 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  5:       1   ORF21 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  6:       1   ORF31 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  7:       1   ORF34 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  8:       1   ORF38 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
##  9:       1   ORF50 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 10:       1   ORF61 0.9985808 0.9996893 0.9692871 0.0005874996 0.0001516189
## 11:       2    ORF2 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 12:       2    ORF3 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 13:       2   ORF11 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 14:       2   ORF14 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 15:       2   ORF18 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 16:       2   ORF26 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 17:       2   ORF28 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 18:       2   ORF29 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 19:       2   ORF39 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 20:       2   ORF40 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 21:       2 ORF66_1 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 22:       2   ORF73 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 23:       2   ORF75 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 24:       2   ORF76 0.8421549 0.9542399 0.7190789 0.0193207434 0.0075520437
## 25:       3    ORF5 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 26:       3    ORF7 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 27:       3   ORF10 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 28:       3   ORF17 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 29:       3   ORF30 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 30:       3   ORF53 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 31:       3   ORF63 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 32:       3  NOIR_2 0.9927129 0.9985552 0.9003588 0.0018794533 0.0004587291
## 33:       4    ORF6 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 34:       4 ORF65_1 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 35:       4 ORF67_1 0.4844426 0.7830124 0.6491845 0.0363760746 0.0224356792
## 36:       5    ORF8 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 37:       5   ORF22 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 38:       5   ORF23 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 39:       5   ORF25 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 40:       5   ORF33 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 41:       5 ORF35.5 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 42:       5   ORF36 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 43:       5     CTO 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 44:       5   ORF42 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 45:       5   ORF43 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 46:       5   ORF44 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 47:       5   ORF46 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 48:       5   ORF58 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 49:       5   ORF62 0.4795512 0.8477928 0.4739086 0.0397567529 0.0180075702
## 50:       6   ORF12 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 51:       6   ORF13 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 52:       6   ORF15 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 53:       6   ORF16 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 54:       6   ORF35 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 55:       6   ORF41 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 56:       6   ORF48 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 57:       6   ORF52 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 58:       6   ORF54 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 59:       6   ORF57 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 60:       6   ORF60 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 61:       6   ORF71 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 62:       6   ORF72 0.8259261 0.9565701 0.6405832 0.0206476430 0.0071277398
## 63:       7   ORF19 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 64:       7   ORF37 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 65:       7   ORF49 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 66:       7   ORF51 0.8160680 0.9495810 0.6700283 0.0214331828 0.0080702454
## 67:       8   ORF24 0.9958735 0.9993909 0.8730728 0.0010785300 0.0001980182
## 68:       8   ORF68 0.9958735 0.9993909 0.8730728 0.0010785300 0.0001980182
## 69:       8   ORF74 0.9958735 0.9993909 0.8730728 0.0010785300 0.0001980182
## 70:       9   ORF27 0.8123167 0.9712173 0.4422435 0.0233352327 0.0052517907
## 71:       9   ORF32 0.8123167 0.9712173 0.4422435 0.0233352327 0.0052517907
## 72:       9   ORF59 0.8123167 0.9712173 0.4422435 0.0233352327 0.0052517907
## 73:      10 ORF64_1 0.8623602 0.9872692 0.3384189 0.0203134193 0.0028130265
## 74:      11  NOIR_1 0.7918505 0.9699239 0.4047690 0.0257680355 0.0055457572
## 75:      12   ORF69 0.7646666 0.9396246 0.5962335 0.0252573471 0.0091709615
## 76:      12   ORF70 0.7646666 0.9396246 0.5962335 0.0252573471 0.0091709615
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c         pchi
##           <num>      <num>     <num>        <num>
##  1: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  2: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  3: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  4: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  5: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  6: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  7: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  8: 0.002101378 -2.6462596 0.7758415 0.0453090771
##  9: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 10: 0.002101378 -2.6462596 0.7758415 0.0453090771
## 11: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 12: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 13: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 14: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 15: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 16: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 17: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 18: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 19: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 20: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 21: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 22: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 23: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 24: 0.004834005 -1.1337702 0.5536628 0.0005830641
## 25: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 26: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 27: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 28: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 29: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 30: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 31: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 32: 0.003469799 -2.1314210 0.8478221 0.4318726350
## 33: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 34: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 35: 0.005060433 -0.5827636 0.1996439 0.0319400222
## 36: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 37: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 38: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 39: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 40: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 41: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 42: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 43: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 44: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 45: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 46: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 47: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 48: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 49: 0.005276687 -0.4807824 0.5462305 0.0847886099
## 50: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 51: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 52: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 53: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 54: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 55: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 56: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 57: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 58: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 59: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 60: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 61: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 62: 0.005151284 -1.0361088 0.6760908 0.1863312328
## 63: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 64: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 65: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 66: 0.005054755 -1.0403978 0.6004065 0.9714841967
## 67: 0.003852134 -2.1878185 1.0467811 0.0826112491
## 68: 0.003852134 -2.1878185 1.0467811 0.0826112491
## 69: 0.003852134 -2.1878185 1.0467811 0.0826112491
## 70: 0.005273787 -0.8768548 1.0221384 0.6101602138
## 71: 0.005273787 -0.8768548 1.0221384 0.6101602138
## 72: 0.005273787 -0.8768548 1.0221384 0.6101602138
## 73: 0.005022019 -0.9087719 1.3255538 0.0684930061
## 74: 0.005200999 -0.8193269 1.0603490 0.2027475766
## 75: 0.005250522 -0.8976199 0.6540101 0.1100175114
## 76: 0.005250522 -0.8976199 0.6540101 0.1100175114
##           se.bp          v         c         pchi

## [1] "ORF48" "ORF19" "ORF49" "ORF69"
## [1] 4
##  [1] "ORF6"    "ORF65_1" "ORF67_1" "ORF8"    "ORF22"   "ORF23"   "ORF25"  
##  [8] "ORF33"   "ORF35.5" "ORF36"   "CTO"     "ORF42"   "ORF43"   "ORF44"  
## [15] "ORF46"   "ORF58"   "ORF62"   "ORF19"   "ORF37"   "ORF49"   "ORF51"  
## [22] "ORF69"   "ORF70"
## [1] 23

Remove genes from clusters ?

##  [1] "ORF6"    "ORF65_1" "ORF67_1" "ORF8"    "ORF22"   "ORF23"   "ORF25"  
##  [8] "ORF33"   "ORF35.5" "ORF36"   "CTO"     "ORF42"   "ORF43"   "ORF44"  
## [15] "ORF46"   "ORF58"   "ORF62"   "ORF19"   "ORF37"   "ORF49"   "ORF51"  
## [22] "ORF69"   "ORF70"
## [1] 23
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       2    14
##  2:       5    14
##  3:       6    13
##  4:       1    10
##  5:       3     8
##  6:       7     4
##  7:       4     3
##  8:       8     3
##  9:       9     3
## 10:      12     2
## 11:      10     1
## 12:      11     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters